I doubt most problems are not Launcher related, the Japanese client had permision problems too, just "easier" to solve since you installed the game where you wanted instead of restricted folders. We just forgot about those problems once we stopped using the official client and used the fanmade tweaker client.
The PSO2JP launcher still has permission issues up to this day. I just verified it.
If the launcher has to write data to disk, they get instantly set to SYSTEM, but the launcher works normally.
It's only AFTER you re-open the launcher, it messes up, throwing "Last Fives".
If the files do exist at this point,
it just carries on no, it also breaks them. Means, once you finished downloading the game, you have to reset ACLs first - then it works up to the next patch or Store intervention.
I assume PSO2NA does exactly the same.